ENG BE 765: Biomedical Optics and Biophotonics
This course surveys the applications of optical science and engineering to a variety of biomedical problems, with emphasis on optical and photonics technologies that enable real, minimally-invasive clinical applications. The course teaches only those aspects of biology itself that are necessary to understand the purpose of the application. The first weeks introduce the optical properties of tissue, and following lectures cover a range of topics in three general areas: 1) Optical spectroscopy applied to diagnosis of cancer and other tissue diseases; 2) Photon migration and optical imaging of subsurface structures in tissue; and 3) Laser-tissue interactions and other applications of light for therapeutic purposes. In addition to formal lectures, recent publications from the literature will be selected as illustrative of various topical areas, and for each publication one student will be assigned to prepare an informal presentation (with overhead slides or PowerPoint) reviewing for the class the underlying principles of that paper and outlining the research results. Same as ENG EC 765; students may not receive credit for both. 4 cr

ENG BE 771: Introduction to Neuroengineering
This course covers existing and future neurotechnologies for analyzing brain signals and for treating neurological and psychiatric diseases. It focuses on the biophysical, biochemical, anatomical principles governing the design of current neurotechnologies, with a goal of encouraging innovations of a new generation of therapies. Topics include basic microscopic and macroscopic architecture of the brain, the fundamental properties of individual neurons and ensemble neural networks, electrophysiology, DBS, TMS, various imaging methods, optical neural control technologies, optogenetics, neuropharmacology, gene therapy, and stem-cell therapy. Discussions of related literatures and design projects will be involved. This course is open to graduate students only and it meets with BE571. 4 cr.

ENG BE 773: Advanced Optical Microscopy and Biological ImagingUndergraduate Prerequisites: ENG BE 401 or ENG EC 401; a background in optics or photonics (ENG EC560 or equivalent) is preferable or permission of instructor.
This course will present a rigorous and detailed overview of the theory of optical microscopy starting from basic notions in light propagation and covering advanced concepts in imaging theory such as Fourier optics and partial coherence. Topics will include basic geometric optics, photometry, diffraction, optical transfer functions, phase contrast microscopy, 3D imaging theory, basic scattering and fluorescence theory, imaging in turbid media, confocal microscopy, optical coherence tomography (OCT), holographic microscopy, fluorescence correlation spectroscopy (FCS), fluorescence resonant energy transfer (FRET), and nonlinear-optics based techniques such as two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) microscopy. Biological applications such as calcium and membrane-potential imaging will be discussed. A background in optics is preferable. A background in signals and analysis is indispensable. In particular, the student should be comfortable with Fourier transforms, complex analysis, and transfer functions. Meets with ENGEC773. Students may not receive credit for both. 4 cr

ENG BE 780: Brain Machine Interfaces
Brain Machine Interfaces introduces major approaches and central challenges in BMI applications. An initial overview will cover low-level details of interfacing with neural tissue, including electrode and optical designs, types of neural signals, and issues of biocompatibility and signal degradation. The core of the course will consider applications, with topics focused on (1) signal decoding approaches in motor control applications, signal to noise requirements, and effects of training and plasticity, and (2) neural stimulation, including choice of peripheral vs. central targets, consequences of topographic organization, types of perceptual responses, and limits to control of distributed systems. Special emphasis will be placed on comparing and critiquing the expanding range of applicable technologies, from in-dwelling microelectrodes to cutting edge neurophotonic tools. To follow rapid changes in the field, course materials will be drawn primarily from research literature. In addition to readings, discussion and computational exercises, students will complete a final project. This is a 4 credit course.

ENG BE 790: Biomedical Engineering SeminarUndergraduate Prerequisites: Required for graduate students in biomedical engineering.
Discussion of current topics in biomedical engineering. Students are expected to read assigned journal articles and to participate actively in weekly discussion meetings. Meetings organized around presentations by invited guests of their research problems, strategy, and technique.

ENG BE 791: PhD Biomedical Engineering Laboratory Rotation SystemUndergraduate Prerequisites: PhD standing in biomedical engineering.
This course allows PhD students to take part in a laboratory rotation system. During these rotations, students become familiar with research activity within departmental laboratories that are of interest to them. These rotations help students identify the laboratory in which they will perform their dissertation research. Postbachelor's PhD students must complete three rotations: one in their first semester of matriculation, and two in their second semester. Post- master's PhD students must complete a minimum of two rotations, one of which must be in their first semester of matriculation. Normally each rotation will last up to seven weeks. Variable cr.

ENG BE 792: Critical Literature ReviewUndergraduate Prerequisites: First year BME PhD graduate students only.
Peer-reviewed publications in the area of biomedical engineering will be critically evaluated. Scientific ethics and the process of review and publication of manuscripts will be discussed. The classes will be a mix of didactic information and group discussion. Methodological issues covered will include study design, techniques used, and interpretation of research findings. Students completing this course will understand the principles underlying preparation and publication of scientific manuscripts and will be able to apply these principles as they read the scientific literature. 2 cr

ENG BE 795: Biomedical Innovation Strategies
This lecture and discussion course will introduce BME graduate students to advanced analylical and strategic planning tools and techniques used by biomedical, biotech, and healthcare companies to anticipate, evaluate, and incorporate breakthrough medical innovations. Senior executives and strategic planners, along with investors, advisors, and clinical innovators will share insights through guest lectures, cases, interviews, and discussions with BME PhD and Masters students interested in biomedical research and product development in the private sector.

ENG BE 801: Teaching PracticumUndergraduate Prerequisites: Students must be in the BME PhD program.
This course cannot be used to meet the structured course requirements. Practical teaching experience for an assigned course, includes some combination of running discussion sections, managing laboratory sections, providing some lectures, preparing homework and solution sets, exams, and grading. Attend lectures/seminars on best teaching practices. 4 cr

ENG BE 900: PhD ResearchUndergraduate Prerequisites: Graduate standing.Graduate Prerequisites: Restricted to pre-prospectus PhD students.
Prerequisite: restricted to pre-prospectus PhD students. Participation in a research project under the direction of a faculty advisor leading to the preparation and defense of a PhD prospectus. Variable cr.

ENG BE 951: Independent StudyUndergraduate Prerequisites: By petition only.
A course of reading under the direction of a faculty advisor covering subject matter not available in a lecture course. Final report or examination normally required. Variable cr

ENG BE 952: Mentored ProjectUndergraduate Prerequisites: Enrollment in the BME MS program.
Students who are pursuing a project to satisfy their practicum requirement for the MS degree will register for up to 4 credits of this course. The course may be taken more than once for up to four credits (ex. two credits in Fall, two credits in Spring). Students will select a suitable project with a mentor that can be completed in 4 credits. The BME Graduate Committee must approve all proposed projects. Each student must write a project report and/or deliver a formal presentation at the end of the course that will be graded by their project mentor. All reports and presentation materials must be received by the BME Graduate Committee.

ENG BE 954: MS ThesisUndergraduate Prerequisites: Graduate Standing.Graduate Prerequisites: Restricted to MS students by petition only.
Participation in a research project under the direction of a faculty advisor leading to the preparation of an original MS thesis. For students pursuing an MS thesis to satisfy the practicum requirement for the MS degree.

ENG BE 991: PhD DissertationUndergraduate Prerequisites: Graduate standing.Graduate Prerequisites: BE 900; restricted to post-prospectus PhD students.
Participation in a research project under the direction of a faculty advisor leading to the preparation and defense of an original PhD dissertation.

ENG BF 527: Appl BioinfmtcsUndergraduate Prerequisites: See course description
This course description is currently under construction.

ENG BF 541: Bioinformatics Internship
Internships provide the bridge between classroom/laboratory study and ?real-world? employment. Each student must complete an internship with a minimum of 400 hours of on-the-job experience (e.g., 10 weeks full-time work in the summer). The format is very flexible, and part-time internships running concurrently with classes or employment are acceptable. Students must consult with their academic advisor to assess the suitability of a proposed internship.

ENG BF 571: Dynamics and Evolution of Biological NetworksGraduate Prerequisites: CAS MA 226 and CAS MA 242; EK102 can be used in lieu of the MA242 pre-req. Familiarity with differential equations and linear algebra at equivalent levels and the consent of instructor can be used in lieu of both pre-reqs.
The course focuses on mathematical models for exploring the organization, dynamics, and evolution of biochemical and genetic networks. Topics include: introductions to metabolic and genetic networks, deterministic and stochastic kinetics of biochemical pathways; genome-scale models of metabolic reaction fluxes; models of regulatory networks; modular architecture of biological networks.

ENG BF 690: Bioinformatics Challenge Project
Project course for first year Bioinformatics graduate students. Open-ended problems will involve bioinformatics as a key element, typically requiring the use of large data sets and computational analysis to make predictions about molecular function, molecular interactions, regulation, etc. Projects will be proposed by the Bioinformatics program faculty and selected by student in teams of three. The end result will be a set of predictions, some of which can be validated retrospectively using data available through online sources and some of which will require experimental validation. During the last 2 months of the academic year, teams will design feasible validation experiments in consultation with the experimental faculty.